pubnet 0.9.1

A python package for storing and working with publication data in graph form.

PubNet publication networks

Provides data types for managing publication networks as a set of graphs.

PubNet provides functions for downloading, storing, manipulating, and saving publication networks. Networks can come from common online sources like pubmed and crossref.

Installation

pip install --user pubnet

More help

See Documentation

Running tests

Installing with poetry install --with=dev,tests --all-extras will install all dependencies needed for running the tests. Then poetry run pytest . will run the test suite.

Optionally, if poetry is not installed, there is a Dockerfile provided. Build the image with docker build --tag poetry:3.12 . then the image can be run with docker run --rm -it -v $PWD:/home/pubnet -w /home/pubnet poetry:3.12. The initial run will download dependencies to .venv inside the directory. After the first run, the dependencies will be reused. It will then run the tests on the current work tree.

This container can also be used to run arbitrary commands without the need to install poetry directly by passing a command to the end of the docker command:

docker run --rm -it -v $PWD:/home/pubnet -w /home/pubnet /bin/bash

In this case, if poetry install hasn't already been run, this will need to be run with the above install command. Then, inside the container, poetry run ipython can be run to start a python repl with pubnet installed.